20-18628153-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_080820.6(DTD1):c.397G>A(p.Val133Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,726 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V133L) has been classified as Uncertain significance.
Frequency
Consequence
NM_080820.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DTD1 | NM_080820.6 | c.397G>A | p.Val133Met | missense_variant | 4/6 | ENST00000377452.4 | |
DTD1 | NM_001318043.2 | c.397G>A | p.Val133Met | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DTD1 | ENST00000377452.4 | c.397G>A | p.Val133Met | missense_variant | 4/6 | 1 | NM_080820.6 | P1 | |
DTD1 | ENST00000494921.2 | c.397G>A | p.Val133Met | missense_variant | 4/5 | 2 | |||
DTD1 | ENST00000647441.1 | c.*60G>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/7 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251368Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135854
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461614Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727056
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.397G>A (p.V133M) alteration is located in exon 4 (coding exon 4) of the DTD1 gene. This alteration results from a G to A substitution at nucleotide position 397, causing the valine (V) at amino acid position 133 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at